DUF3565 - PFAM28P - GREMLIN Contacts

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DUF3565 - Protein of unknown function (DUF3565)

PFAM:	PF12088	Sequences: VGFHQDEEGDWVAELECGHTQHVRHDPPWQNRPWVLTEEGRASRLGTELDCKKCDEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (57)
Sequences:	3690 (1999)
Seq/√Len:	264.7
META:	0.942

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_H	14_E	3.916	1.00
14_E	20_T	2.994	1.00
50_D	55_D	2.696	1.00
37_T	40_G	2.686	1.00
38_E	42_A	2.625	1.00
44_R	47_T	2.506	1.00
4_H	20_T	2.495	1.00
4_H	12_V	2.360	1.00
26_D	30_Q	2.343	1.00
20_T	53_K	2.018	1.00
52_K	56_E	1.987	1.00
5_Q	9_G	1.828	1.00
23_V	49_L	1.789	1.00
10_D	26_D	1.706	1.00
40_G	43_S	1.555	1.00
5_Q	11_W	1.449	1.00
53_K	57_G	1.303	1.00
25_H	36_L	1.283	1.00
2_G	14_E	1.243	1.00
3_F	23_V	1.139	1.00
39_E	42_A	1.119	1.00
26_D	29_W	0.982	1.00
53_K	56_E	0.973	1.00
29_W	36_L	0.971	1.00
18_G	31_N	0.943	1.00
12_V	20_T	0.912	1.00
29_W	32_R	0.898	1.00
52_K	55_D	0.892	1.00
16_E	31_N	0.882	1.00
39_E	43_S	0.873	1.00
24_R	28_P	0.871	1.00
21_Q	52_K	0.866	1.00
33_P	36_L	0.821	0.99
22_H	25_H	0.821	0.99
12_V	29_W	0.816	0.99
51_C	54_C	0.786	0.99
21_Q	30_Q	0.744	0.99
21_Q	32_R	0.740	0.99
18_G	29_W	0.730	0.99
28_P	35_V	0.728	0.99
22_H	27_P	0.709	0.98
42_A	45_L	0.700	0.98
49_L	52_K	0.694	0.98
23_V	32_R	0.690	0.98
21_Q	25_H	0.686	0.98
41_R	46_G	0.685	0.98
16_E	53_K	0.678	0.98
2_G	15_L	0.650	0.97
20_T	57_G	0.648	0.97
10_D	32_R	0.647	0.97
13_A	49_L	0.639	0.97
28_P	34_W	0.614	0.96
25_H	28_P	0.609	0.96
24_R	27_P	0.602	0.95
43_S	48_E	0.588	0.95
50_D	56_E	0.588	0.95
8_E	47_T	0.580	0.94
2_G	45_L	0.578	0.94
35_V	43_S	0.576	0.94
22_H	28_P	0.572	0.94
7_E	55_D	0.571	0.94
30_Q	44_R	0.566	0.93
21_Q	24_R	0.565	0.93
14_E	53_K	0.562	0.93
15_L	23_V	0.559	0.93
18_G	57_G	0.559	0.93
33_P	37_T	0.556	0.93
43_S	56_E	0.556	0.93
6_D	13_A	0.555	0.93
18_G	36_L	0.554	0.93
23_V	35_V	0.553	0.93
40_G	44_R	0.546	0.92
16_E	56_E	0.538	0.92
15_L	28_P	0.536	0.92
3_F	47_T	0.533	0.91
30_Q	57_G	0.532	0.91
45_L	55_D	0.531	0.91
32_R	36_L	0.527	0.91
40_G	45_L	0.522	0.90
5_Q	16_E	0.522	0.90
17_C	46_G	0.512	0.90
6_D	11_W	0.511	0.90
16_E	55_D	0.507	0.89
47_T	53_K	0.504	0.89
32_R	55_D	0.503	0.89
20_T	56_E	0.500	0.88

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1z84A	2	0.5614	15.2	0.896	Contact Map
1gupA	2	0.7544	14.6	0.897	Contact Map
4r2yA	4	0.7895	7.1	0.91	Contact Map
2l0bA	1	0.7368	6.6	0.912	Contact Map
2y1nA	1	0.7018	6.5	0.912	Contact Map
4a0kB	1	0	6	0.913	Contact Map
1hxrA	1	0.3684	5.6	0.915	Contact Map
4ui9B	1	0.7895	5.2	0.916	Contact Map
2kizA	1	0.7368	5.1	0.916	Contact Map
3dplR	1	0.6842	4.8	0.917	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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